Blindly tinkering with the microbiome is, however, exactly what some researchers say we have been doing, willy-nilly, for more than 70 years, since the dawn of the antibiotic era. For Martin Blaser, a physician at New York University’s School of Medicine, one trend stands out: The typical child in the developed world now receives 10 to 20 courses of antibiotic treatment by the age of 18, often for conditions where these drugs do little or no good. “For two or three generations we’ve been under the illusion that there is no long-term cost to using antibiotics,” says Blaser, eyebrows rising over the tops of his wire-rimmed eyeglasses. It certainly hasn’t seemed like a cost for the child being treated, and only remotely for society at large (because excess use can lead to antibiotic resistance). But “you can’t have something this powerful,” says Blaser, “and change something as fundamental as our microbiome, at a critical time in development, and not have an effect.”

Though they have always known that antibiotics kill “good” bacteria as well as “bad,” doctors generally assumed the body’s microbial community was resilient enough to bounce back. But new studies show that the microbiome struggles to recover from repeated assaults, and may lose species permanently. Blaser suspects that diversity loss is cumulative, worsening from one generation to the next. He calls it “the disappearing microbiota hypothesis.” It’s like somebody played the piano solo with a two-by-four.

Along with the antibiotics, Blaser blames our obsession with cleanliness and antibacterial soaps and lotions. In addition, about 30 percent of American children are now born by Caesarean section. They start life without the microbiome they would normally have picked up passing through the mother’s birth canal, and some research suggests that this puts them at a disadvantage. Studies show that a diverse microbial community is essential to jump-start a baby’s immune system, establish a healthy digestive tract and even help shape the growing brain. Blaser doesn’t think it’s a coincidence that children now face an epidemic of medical disorders in all these areas, and that the surge in incidence tracks with an increase in Caesarean births and the introduction of powerful new antibiotics in the 1970s and ’80s.

“Here’s the point,” he says. “You have 10 or 12 diseases that are all going up dramatically, more or less in parallel—diabetes, obesity, asthma, food allergies, hay fever, eczema, celiac disease. They’re not going up 2 or 3 percent, they’re doubling and quadrupling. Each one may have a different cause. Or there could be one cause that’s providing the fuel, and my hypothesis is that it’s the disappearing microbiota.”

For Blaser, the decline of one “bad” bacterial species represents what’s happening to the entire microbiome. Helicobacter pylori, which lives in the human stomach, became notorious in the 1980s after scientists demonstrated that it is the essential precondition for almost all peptic ulcers and stomach cancers. The microbe was already on the decline from sanitary improvements and routine antibiotic use, but doctors then began directly targeting H. pylori in adults, incidentally meaning parents were less likely to pass the microbe on to their children. Today, while up to 100 percent of children in developing countries have Helicobacter, only about 6 percent of American kids do—and the latter is ostensibly a good thing.

“It’s good and it’s bad,” says Blaser. A study last year traced the human association with H. pylori back at least 116,000 years into our evolutionary history. “The idea that an organism that has been with us that long is disappearing in a century is striking,” says Blaser. “The good news is that it means less ulcers and less gastric cancer. The bad news is that it means more childhood-onset asthma and more esophageal reflux.” In certain circumstances, at certain times, Blaser argues, H. pylori may have protective effects not yet fully recognized.

The medical community has thus far resisted the rehabilitation of H. pylori. When Blaser first proposed that doctors would eventually find themselves reintroducing the species into American children, David Y. Graham, a gastroenterologist at the Baylor College of Medicine, replied in print, “The only good Helicobacter pylori is a dead Helicobacter pylori.” Of Blaser, he says, “He’s good at selling things.” Graham thinks Blaser is wrong to ascribe beneficial effects to H. pylori, and he worries Blaser’s message will dissuade people from seeking needed treatments.

Douglas Morgan, a Vanderbilt University gastroenterologist and epidemiologist, credits Blaser with pointing out the dual character of H. pylori. But the species may just look like the key player protecting against immune disorders because a simple medical test makes it the easiest to measure. Other microbes that rise and fall along with it could really drive the process, Morgan says.

Still, the attack on antibiotics doesn’t come casually. Blaser is a past president of the Infectious Diseases Society of America. Physicians who share his medical specialty depend utterly on anti­biotics to treat patients suffering from pneumonia, heart valve infections and a deadly host of other disorders. But infectious disease specialists also see the cost being paid for their reliance on antibiotics, says Relman, a fellow microbiome researcher, physician and current president of the Infectious Diseases Society. These doctors have become dismayingly accustomed to saving patients’ lives, he says, only to see them go home and develop a crippling and sometimes fatal case of Clostridium difficile. “C. diff.,” as it’s known, is an intestinal infection with chronic diarrhea, and incidence in the United States has more than doubled since 2000. The problem almost always results from antibiotic use that has destroyed the normal population of microbes, clearing the way for just one, C. difficile, to dominate. So far, the only conventional remedy is another antibiotic.